Variant report

Variant	rs41290716
Chromosome Location	chr3:49717795-49717796
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49717605-49717817	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:49717503-49727239	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:49717166-49718619	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:49717629-49717823	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:49716580-49724829	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49717546-49718796	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:49716559-49721545	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:49716518-49723590	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:49717656-49717820	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49715479..49718306-chr3:49759884..49762675,3	K562	blood:
2	chr3:49715211..49719699-chr3:49722366..49724649,4	K562	blood:
3	chr3:49581837..49584677-chr3:49716842..49719097,2	MCF-7	breast:
4	chr3:49715255..49718446-chr3:49718549..49721372,3	MCF-7	breast:

No data

Variant related genes	Relation type
APEH	TF binding region
ENSG00000173540	Chromatin interaction
ENSG00000259970	Chromatin interaction
ENSG00000173531	Chromatin interaction
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs62259945	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62260717	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62261251	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262670	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49712200-49723800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49712800-49722200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:49712800-49722200	Strong transcription	Fetal Stomach	stomach
4	chr3:49712800-49723600	Weak transcription	Right Atrium	heart
5	chr3:49712800-49726200	Weak transcription	Small Intestine	intestine
6	chr3:49713000-49718400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:49713000-49721200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49713000-49721400	Strong transcription	NHEK	skin
9	chr3:49713000-49721600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:49713000-49721600	Strong transcription	Brain Substantia Nigra	brain
11	chr3:49713000-49721600	Strong transcription	NHLF	lung
12	chr3:49713000-49722000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:49713000-49722000	Strong transcription	Stomach Smooth Muscle	stomach
14	chr3:49713000-49722200	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:49713000-49722400	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr3:49713000-49722400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:49713000-49722600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:49713000-49722800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:49713000-49722800	Strong transcription	Thymus	Thymus
20	chr3:49713000-49723200	Weak transcription	Stomach Mucosa	stomach
21	chr3:49713000-49723400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:49713000-49723800	Weak transcription	Fetal Heart	heart
23	chr3:49713200-49720600	Strong transcription	Osteobl	bone
24	chr3:49713200-49721400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:49713200-49721400	Strong transcription	Colon Smooth Muscle	Colon
26	chr3:49713200-49721400	Strong transcription	Left Ventricle	heart
27	chr3:49713200-49721600	Strong transcription	Rectal Smooth Muscle	rectum
28	chr3:49713200-49721800	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:49713200-49721800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:49713200-49722000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:49713200-49722000	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr3:49713200-49722000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:49713200-49722200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:49713200-49722200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:49713200-49722200	Strong transcription	Placenta	Placenta
36	chr3:49713200-49722400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:49713200-49722400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:49713200-49722400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:49713200-49722400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:49713200-49722400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:49713200-49722600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:49713200-49722600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:49713200-49722600	Strong transcription	Brain Germinal Matrix	brain
44	chr3:49713200-49722800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:49713200-49723000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:49713200-49723000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:49713400-49719800	Strong transcription	Lung	lung
48	chr3:49713400-49720200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:49713400-49721400	Strong transcription	Aorta	Aorta
50	chr3:49713400-49721400	Strong transcription	Hela-S3	cervix

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